GEEVS Data Analysis (Beta Version)

Aggregation of variant frequencies from multiple studies has been done separately for Illumina and Solid platform based calls. Illumina based SNV calls have been produced by GATK UnifiedGenotyper's multi-sample calling, separately for each study of at least 50 cases. Resulting VCF files need to fulfill various filter criteria to be considered for aggregation, e.g. percent recall in dbSNP, TiTv ratio as well as high correlation to 1000genomes and EVS. Furthermore all reported variants are filtered in the following manner:

Some aggregation statistics are given below.

Percentage of known for SNVs and INDELs (dbSNP v.138)

Gatk_report_known

Transition/Transversion (TiTv) ratio for SNVs

Gatk_report.titv

SNV allele frequency correlation of GEEVS vs. Exome Variant Server (EVS) and GEEVS vs. 1000 Genomes

Qc_maf_plots_snps

INDEL allele frequency correlation of GEEVS vs. Exome Variant Server (EVS) and GEEVS vs. 1000 Genomes

Qc_maf_plots_indels